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Analysis of gene expression in the rel- relA+ and the rel- relAE335Q strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

ABSTRACT: We investigated the role of basal ppGpp levels in Synechococcus elongatus PCC7942 in adaptation to darkness. We performed RNA-seq experiments using the rel- relA+ and the rel- relAE335Q strain at dusk and during exposure to 12 h of darkness. We show that basal ppGpp levels is not sufficient for restoration of appropriate transcriptional shutdown in response to darkness.

ORGANISM(S): Synechococcus elongatus PCC 7942 = FACHB-805

PROVIDER: GSE105774 | GEO | 2017/12/12

SECONDARY ACCESSION(S): PRJNA415380

REPOSITORIES: GEO

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Analysis of gene expression in wild type and the rel- strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

Project description:We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed RNA-seq experiments using wild type and the rel- strain at dusk and during exposure to 12 h of darkness. We show that ppGpp is required for correct response to darkness.

2017-12-12 | GSE103704 | GEO

Analysis of RNA polymerase stalling index in wild type and the rel- strain of Synechococcus elongatus PCC7942 - chromatin immunoprecipitation followed by sequencing during exposure to darkness (cells grown in light/dark conditions)

Project description:We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed ChIP-seq experiments using wild type and the rel- strain at dusk, during exposure to 12 h of darkness and at dawn. We show that the RNA polymerase pausing index is globally lower in the rel- strain.

2017-12-12 | GSE106824 | GEO

Analysis of gene expression in the wild type and rel- strains of Synechococcus elongatus PCC7942 with RNA sequencing during constant light conditions

Project description:Rel is an enzyme involved in the metabolism of ppGpp. We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light and after exposure to darkness. We performed RNA-seq experiments using the rel- strain and wild type and show that ppGpp is required for regulation of global transcription in light and in darkness.

2017-12-12 | GSE103462 | GEO

Analysis of gene expression in the rel- + relA+ and rel- + relAE335Q strains of Synechococcus elongatus PCC7942 with RNA sequencing during constant light conditions

Project description:We investigated the role of the basal levels of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using the rel- + relA+ and rel- + relAE335Q strains and show that basal levels of ppGpp are required for regulation of global transcription in light.

2017-12-12 | GSE103463 | GEO

Gene expression in the wild type + relA+ and wild type + relAE335Q strains of Synechococcus elongatus PCC7942 after induction of expression of RelA+ or RelAE335Q with theophylline at subjective dusk - RNA sequencing during constant light conditions

Project description:We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using wild type + relA+ and wild type + relAE335Q strains after induction with theophylline starting at subjective dusk. We show that ppGpp induction inhibits global transcription in light.

2017-12-12 | GSE103644 | GEO

Analysis of gene expression in the rel- relA+ and the rel- relAE335Q strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

Project description:Analysis of gene expression in the rel- relA+ and the rel- relAE335Q strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

| PRJNA415380 | ENA

Transcriptome analysis of a model cyanobacterium Synechococcus elongatus PCC7942 under salt stress and protein synthesis-inhibiting stress conditions

Project description:Here, we treated the model cyanobacterium Synechococcus elongatus PCC7942 with streptomycin, which selectively binds to bacterial ribosomes, at a concentration of 50 µg/mL and performed transcriptome analysis using RNA sequencing. In addition to antibiotic stress, we treated salt stress (0.4 M NaCl) and performed RNA sequencing analysis.

2023-05-17 | GSE225426 | GEO

ppGpp controls global gene expression in light and in darkness in S. elongatus

Project description:ppGpp controls global gene expression in light and in darkness in S. elongatus

| PRJNA402060 | ENA

Project description:Analysis of RNA polymerase stalling index in wild type and the rel- strain of Synechococcus elongatus PCC7942 - chromatin immunoprecipitation followed by sequencing during exposure to darkness (cells grown in light/dark conditions)

| PRJNA418146 | ENA

Gene expression analysis of rel knockout and dcpA knockout strains of Mycobacterium smegmatis MC2 155

Project description:The experiment was carried out to study the effect of loss of (p)ppGpp or cyclic di-GMP on the gene expression pattern of Mycobacterium smegmatis MC2 155 strains. The cells were cultured in MB7H9 broth containing 0.2% glycerol and 0.05% Tween 80. The transcriptome analysis was performed using GeneSpring GX12 software. Fold changes were calculated with respect to the median expression of wild type replicates. The number of differentially expressed genes (p <0.1) in rel knockout were 417 whereas those in dcpA knockout were 149. Earlier studies had shown that rel knockout and dcpA knockout had shown lower levels of glycopeptidolipids and polar lipids in the cell wall. The microarray data also corraborates our current findings. Organism : Mycobacterium smegmatis, Agilent Custom Mycobacterium smegmatis Gene Expression M.smegmatis_gxp_8X15K (AMADID: 029929) designed by Genotypic Technology Private Limited.

2015-06-10 | E-GEOD-69681 | biostudies-arrayexpress

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